Tracking vectors of bacteria and phytoplasmas threatening Europe's major crops

Success story of the Euphresco project 'Tracking vectors of bacteria and phytoplasmas threatening Europe’s major crops

Potato virus Y (PVY) strains in Belgian seed potatoes and first molecular detection of the N-Wi strain

Potato virus Y (PVY), one of the most important agents causing potato crop losses worldwide, is transmitted by a variety of aphid species in a non-persistent manner. Several PVY strains have been differentiated, all of them causing different symptoms and symptom expression levels on numerous commercial potato cultivars. In Belgium, strains belonging to the N group have been reported as the most prevalent, but no detailed information on the relative importance of the PVY strains in Belgium have been published to date. We report here on a survey performed on Belgian seed potatoes harvested in 2010 in which 2700 individual tubers from 54 seed potato lots originating from 54 farms were screened for presence of PVY. The results revealed a high PVY incidence and substantial strain diversity in some farms. The dominance of the N group in Belgian seed potatoes was confirmed, while the 0 strain was only found in a few locations. Further characterization using multiplex PCR identified 75% of the isolates as NTN strains and 7.5% as Wilga strain (N-Wi). The presence of the N-Wi strain was confirmed and characterized for the first time in Belgian seed potato production

Whole-genome deep sequencing reveals host-driven in-planta evolution of Columnea Latent Viroid (CLVd) quasi-species populations

Columnea latent viroid (CLVd) is one of the most serious tomato diseases. In general, viroids have high mutation rates. This generates a population of variants (so-called quasi-species) that co-exist in their host and exhibit a huge level of genetic diversity. To study the population of CLVd in individual host plants, we used amplicon sequencing using specific CLVd primers linked with a sample-specific index sequence to amplify libraries. An infectious clone of a CLVd isolate Chaipayon-1 was inoculated on different solanaceous host plants. Six replicates of the amplicon sequencing results showed very high reproducibility. On average, we obtained 133,449 CLVd reads per PCR-replicate and 79 to 561 viroid sequence variants, depending on the plant species. We identified 19 major variants (>1.0% mean relative abundance) in which a total of 16 single-nucleotide polymorphisms (SNPs) and two single nucleotide insertions were observed. All major variants contained a combination of 4 to 6 SNPs. Secondary structure prediction clustered all major variants into a tomato/bolo maka group with four loops (I, II, IV and V), and a chili pepper group with four loops (I, III, IV and V) at the terminal right domain, compared to the CLVd Chaipayon-1 which consists of five loops (I, II, III, IV and V)

Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

The widespread use of High-Throughput Sequencing (HTS) for detection of plant viruses and sequencing of plant virus genomes has led to the generation of large amounts of data and of bioinformatics challenges to process them. Many bioinformatics pipelines for virus detection are available, making the choice of a suitable one difficult. A robust benchmarking is needed for the unbiased comparison of the pipelines, but there is currently a lack of reference datasets that could be used for this purpose. We present 7 semi-artificial datasets composed of real RNA-seq datasets from virus-infected plants spiked with artificial virus reads. Each dataset addresses challenges that could prevent virus detection. We also present 3 real datasets showing a challenging virus composition as well as 8 completely artificial datasets to test haplotype reconstruction software. With these datasets that address several diagnostic challenges, we hope to encourage virologists, diagnosticians and bioinformaticians to evaluate and benchmark their pipeline(s)

Publisher Correction: Science diplomacy for plant health

Correction to: Nature Plants https://doi.org/10.1038/s41477-020-0744-x, published online 11 August 2020.1 Pág.An amendment to this paper has been published and can be accessed via a link at the top of the paper.In the version of this Comment originally published, in the penultimate paragraph of the section “Steps towards global phytosanitary research coordination” the second sentence incorrectly defined IPPC as ‘Intergovernmental Panel on Climate Change’, though it was cor rectly defined earlier as ‘International Plant Protection Convention’; the sentence has now been corrected to read “Ideally, they should benefit from the reputation of a United Nations mandate convention, such as the IPPC…”Peer reviewe